as_subfeats | R Documentation |
Read subfeat data such as domains or blast hits on genes into a tidy
dataframe. Subfeats need to be associated with an already added feat
track. The subfeat track itself is internally converted into a new,
regular feat track by mapping the start
and end
coordinates provided
relative to their parent feat into coordinates relative to the sequences
underlying the parent feats.
as_subfeats(x, seqs, feats, ..., everything = TRUE)
## S3 method for class 'tbl_df'
as_subfeats(
x,
seqs,
feats,
...,
everything = TRUE,
transform = c("none", "aa2nuc", "nuc2aa")
)
x |
subfeat data convertible to a feat layout |
seqs |
the sequence layout the parent feats map onto. |
feats |
the parent feats the subfeats map onto. |
... |
passed on to |
everything |
set to FALSE to drop optional columns |
transform |
use if feats and subfeats are in different coordinate |
Obligatory columns are feat_id
, start
and end
. Also recognized are
strand
and bin_id
.
Note start
and end
for every record will be coerced so that start < end
. If no strand
was provided, strand
will be added and set to "+" for
records that initially had start < end
and "-" for end < start
inputs. If
strand
was provided, start
and end
will be reorganized to conform with
start < end
without any additional effect.
a tbl_df with plot coordinates
as_subfeats(tbl_df)
: Convert a list of tibbles into a feat layout
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